Protests of the anthem by NFL players, almost all African American, began last year when the then 49ers quarterback Colin Kaepernick kneeled in protest against racial injustice and police brutality. 49ers players have been prominent among those kneeling this season and could have been expected to kneel on Sunday.

Nor was Pence scheduled to take in the whole game. Air Force Two was due to take off from Indianapolis international airport at 4pm on Sunday, in order for the vice-president to attend a political fundraiser in Los Angeles. The Colts-49ers game kicked off at 1pm ET and finished after 4.30pm, after going to overtime.

At a rally in Alabama last month, Trump launched aggressive criticism of players and the NFL. Though Kaepernick had knelt to protest against unpunished police killings of African Americans, the president and the White House insisted that protesting during the anthem showed disrespect to the flag and to American troops, veterans and first responders.

Senior administration figures including the treasury secretary, Stephen Mnuchin, and attorney general, Jeff Sessions, were deployed to say that in this instance, freedom of speech did not apply. In response, large numbers of players kneeled, teams coordinated actions and owners criticised Trump’s words.

Though debate continued about the meaning of the protests, until Pence’s walkout the issue had seemed to be receding from public view.

Players and some NFL writers think Kaepernick, who took the 49ers to the Super Bowl in 2013, has been blackballed by the league. On Sunday, CBS reported that he said he would not protest during the anthem if he ever returned. The reporter then retracted the story and Kaepernick tweeted a quote attributed to – but not coined by – Winston Churchill: “A lie gets halfway around the world before the truth has a chance to get its pants on.”

Members of the San Francisco 49ers kneel during the playing of the national anthem. Photograph: Michael Conroy/AP

Many observers have also accused the president of seeking to use the NFL protests as a distraction from his own political woes.

Trump has recently been criticised for his response to the catastrophic effect of Hurricane Maria on Puerto Rico, for his approach to North Korea, and over his relationship with the secretary of state, Rex Tillerson. On Sunday, the president was embroiled in an embarrassing exchange of insults with Bob Corker, the chair of the Senate foreign relations committee and a senior member of Republican leadership.

In the statement issued by the White House, Pence said: “I left today’s Colts game because President Trump and I will not dignify any event that disrespects our soldiers, our Flag, or our National Anthem.”

It read: “At a time when so many Americans are inspiring our nation with their courage, resolve, and resilience, now, more than ever, we should rally around our flag and everything that unites us.”

The White House released a picture of Pence and his wife standing for the anthem at the stadium in Indianapolis, with their hands on their hearts.

Pence’s Las Vegas visit meant he missed an unveiling of a statue of the great Indianapolis quarterback Peyton Manning on Saturday. Manning’s jersey was retired on Sunday.

On Monday morning, Trump showed no sign of letting the issue go, tweeting: “The trip by Pence was long planned. He is receiving great praise for leaving game after the players showed such disrespect for country!”